Evaluate gene sets by cell type-specific gene expression

Setup

Load R libraries

library(data.table)
library(ggplot2)
library(ggpubr)
library(tidyr)
library(limma)
library(stringr)

theme_set(theme_classic())

cell_type_name = params$cell_type_name
graph_weight = params$graph_weight

cell_type_name

## [1] "Astro"

graph_weight

## [1] "10.0"

Check the expression of each gene set in each brain-related cell type

Read in gene info and gene set assignments

file_tag = sprintf("%s_%s", cell_type_name, graph_weight)

assayed_genes = scan(sprintf("output/gene_list_%s.txt", file_tag), 
                     what = character(), sep="\n")

length(assayed_genes)

## [1] 2000

gene_sets = scan(sprintf("output/name_s_%s.txt", file_tag), 
                 what = character(), sep="\n")

gene_sets = sapply(gene_sets, strsplit, split=",")
n_genes   = sapply(gene_sets, length)
names(n_genes) = NULL
summary(n_genes)

##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##    39.0    42.0    43.0    42.9    44.0    45.0

length(n_genes)

## [1] 40

sort(n_genes)

##  [1] 39 40 41 41 41 41 41 41 41 42 42 42 42 42 43 43 43 43 43 43 43 43 44 44 44
## [26] 44 44 44 44 44 44 44 44 44 44 44 45 45 45 45

Find gene symbols using the alias2Symbol function from limma.

a2s = rep(NA, length(assayed_genes))
for(i in 1:length(assayed_genes)){
  gi = assayed_genes[i]
  ai = alias2Symbol(gi)
  if(length(ai) > 1){
    print(gi)
    print(ai)
  }
  a2s[i] = ai[1]
}

## [1] "MPP6"
## [1] "MPHOSPH6" "PALS2"

table(is.na(a2s))

## 
## FALSE  TRUE 
##  1643   357

table(a2s == assayed_genes, useNA = 'ifany')

## 
## FALSE  TRUE  <NA> 
##    21  1622   357

gene_info = data.table(sym_in_data = assayed_genes, sym_limma = a2s)

gene_info[sym_in_data != sym_limma,]

##      sym_in_data   sym_limma
##  1:       BTBD11       ABTB3
##  2:    LINC01006    RNF32-DT
##  3:    LINC01185      REL-DT
##  4:   ZRANB2-AS2   ZRANB2-DT
##  5:    LINC00271     AHI1-DT
##  6:     RFX3-AS1     RFX3-DT
##  7:    COX10-AS1    COX10-DT
##  8:   SUCLG2-AS1   SUCLG2-DT
##  9:      C5orf17   LINC02899
## 10:     OSMR-AS1     OSMR-DT
## 11:  C8orf37-AS1 CFAP418-AS1
## 12: CTB-178M22.2   TENM2-AS1
## 13:    LINC00637 PPP1R13B-DT
## 14:         MPP6    MPHOSPH6
## 15:      C7orf61      SPACDR
## 16:      C3orf35       APRG1
## 17:       HRAT92    PDGFA-DT
## 18:    LINC00884  ATP13A3-DT
## 19:    LINC01137  ZC3H12A-DT
## 20: TMEM161B-AS1 TMEM161B-DT
## 21:      MAFG-DT       MILIP
##      sym_in_data   sym_limma

gene_info[, gene_symbol := sym_in_data]
gene_info[which(sym_in_data != sym_limma & (gene_symbol != "MT-CO2")), 
                gene_symbol := sym_limma]

dim(gene_info)

## [1] 2000    3

gene_info[1:5,]

##    sym_in_data sym_limma gene_symbol
## 1:        CD38      CD38        CD38
## 2:     PRKAR2B   PRKAR2B     PRKAR2B
## 3:        ASB4      ASB4        ASB4
## 4:       USH1C     USH1C       USH1C
## 5:    ARHGAP44  ARHGAP44    ARHGAP44

t1 = table(gene_info$gene_symbol)
table(t1)

## t1
##    1 
## 2000

Read in cell type-specific expression data

Gene set annotations (by gene symbols) were downloaded from MSigDB website.

ct = fread("../Annotation/rna_single_cell_type.tsv.gz")
dim(ct)

## [1] 1587110       4

ct[1:5,]

##               Gene Gene name             Cell type  nTPM
## 1: ENSG00000000003    TSPAN6            Adipocytes 149.5
## 2: ENSG00000000003    TSPAN6 Alveolar cells type 1   6.1
## 3: ENSG00000000003    TSPAN6 Alveolar cells type 2  10.5
## 4: ENSG00000000003    TSPAN6            Astrocytes  13.9
## 5: ENSG00000000003    TSPAN6               B-cells   1.5

length(unique(ct$`Cell type`))

## [1] 79

table(ct$`Cell type`)

## 
##                      Adipocytes           Alveolar cells type 1 
##                           20090                           20090 
##           Alveolar cells type 2                      Astrocytes 
##                           20090                           20090 
##                         B-cells             Basal keratinocytes 
##                           20090                           20090 
##           Basal prostatic cells         Basal respiratory cells 
##                           20090                           20090 
## Basal squamous epithelial cells                   Bipolar cells 
##                           20090                           20090 
##          Breast glandular cells      Breast myoepithelial cells 
##                           20090                           20090 
##                  Cardiomyocytes                  Cholangiocytes 
##                           20090                           20090 
##                      Club cells           Collecting duct cells 
##                           20090                           20090 
##        Cone photoreceptor cells                Cytotrophoblasts 
##                           20090                           20090 
##                 dendritic cells              Distal enterocytes 
##                           20090                           20090 
##            Distal tubular cells                    Ductal cells 
##                           20090                           20090 
##                Early spermatids      Endometrial ciliated cells 
##                           20090                           20090 
##       Endometrial stromal cells               Endothelial cells 
##                           20090                           20090 
##           Enteroendocrine cells                 Erythroid cells 
##                           20090                           20090 
##              Excitatory neurons        Exocrine glandular cells 
##                           20090                           20090 
##       Extravillous trophoblasts                     Fibroblasts 
##                           20090                           20090 
##   Gastric mucus-secreting cells     Glandular and luminal cells 
##                           20090                           20090 
##                    granulocytes                 Granulosa cells 
##                           20090                           20090 
##                     Hepatocytes                  Hofbauer cells 
##                           20090                           20090 
##                Horizontal cells              Inhibitory neurons 
##                           20090                           20090 
##         Intestinal goblet cells                       Ionocytes 
##                           20090                           20090 
##                   Kupffer cells                Langerhans cells 
##                           20090                           20090 
##                 Late spermatids                    Leydig cells 
##                           20090                           20090 
##                     Macrophages                     Melanocytes 
##                           20090                           20090 
##                Microglial cells                       monocytes 
##                           20090                           20090 
##           Mucus glandular cells               Muller glia cells 
##                           20090                           20090 
##                        NK-cells Oligodendrocyte precursor cells 
##                           20090                           20090 
##                Oligodendrocytes      Pancreatic endocrine cells 
##                           20090                           20090 
##                    Paneth cells               Peritubular cells 
##                           20090                           20090 
##                    Plasma cells       Prostatic glandular cells 
##                           20090                           20090 
##            Proximal enterocytes          Proximal tubular cells 
##                           20090                           20090 
##      Respiratory ciliated cells         Rod photoreceptor cells 
##                           20090                           20090 
##             Salivary duct cells                   Schwann cells 
##                           20090                           20090 
##          Serous glandular cells                   Sertoli cells 
##                           20090                           20090 
##               Skeletal myocytes             Smooth muscle cells 
##                           20090                           20090 
##                   Spermatocytes                   Spermatogonia 
##                           20090                           20090 
##       Squamous epithelial cells        Suprabasal keratinocytes 
##                           20090                           20090 
##            Syncytiotrophoblasts                         T-cells 
##                           20090                           20090 
##                     Theca cells         Thymic epithelial cells 
##                           20090                           20090 
##          Undifferentiated cells 
##                           20090

cell_group = fread("../Annotation/rna_single_cell_type_brain.tsv")
dim(cell_group)

## [1] 16  2

cell_group[1:2,]

##             Cell_type Cell_group
## 1: Excitatory neurons   Neuronal
## 2: Inhibitory neurons   Neuronal

ct = ct[`Cell type` %in% cell_group$Cell_type,]
table(ct$`Cell type`)

## 
##                      Astrocytes                         B-cells 
##                           20090                           20090 
##                   Bipolar cells        Cone photoreceptor cells 
##                           20090                           20090 
##              Excitatory neurons                Horizontal cells 
##                           20090                           20090 
##              Inhibitory neurons                Microglial cells 
##                           20090                           20090 
##               Muller glia cells Oligodendrocyte precursor cells 
##                           20090                           20090 
##                Oligodendrocytes                    Plasma cells 
##                           20090                           20090 
##         Rod photoreceptor cells                   Schwann cells 
##                           20090                           20090 
##                         T-cells 
##                           20090

Check gene expression for each gene set

dim(gene_info)

## [1] 2000    3

for(k in 1:length(gene_sets)){
  if(length(gene_sets[[k]]) < 10) { next }
  
  print(k)
  set_k = paste0("set_", k)
  print(gene_sets[[k]])
  
  genes = gene_info[sym_in_data %in% gene_sets[[k]], gene_symbol]

  n_genes = sum(genes %in% ct$`Gene name`)
  print(sprintf("found %d genes.", n_genes))

  if(n_genes == 0) { next }

  df = ct[`Gene name` %in% genes,]
  dim(df)
  df[1:2,]
  
  stopifnot(all(str_to_lower(df$`Cell type`) %in% 
                  str_to_lower(cell_group$Cell_type)))
  
  mat1 = match(str_to_lower(df$`Cell type`), 
               str_to_lower(cell_group$Cell_type))
  
  df = cbind(df, cell_group[mat1,])
  df[1:2,]
  
  df$Cell_type = factor(df$Cell_type, levels = cell_group$Cell_type)
  df$Cell_group = factor(df$Cell_group, 
                         levels = unique(cell_group$Cell_group))
  
  p1 = ggplot(df, aes(x=Cell_type, y=log10(nTPM + 0.1), fill=Cell_group)) + 
    geom_boxplot() + xlab("Cell type") + ggtitle(set_k) + 
    theme(axis.text.x = element_text(angle = 45, hjust = 1)) + 
    scale_fill_brewer(palette="RdBu")

  print(p1)
}

## [1] 1
##  [1] "MYO16"    "AMPH"     "PPEF1"    "SGK2"     "FRK"      "SIPA1L2" 
##  [7] "APOC1"    "MON1A"    "CES2"     "ZNF497"   "RAB39A"   "IL1RAPL2"
## [13] "ITGA3"    "CCDC124"  "SYN1"     "NGEF"     "PPP1R15A" "CASS4"   
## [19] "EPHB6"    "SUSD1"    "CHD5"     "DUSP1"    "KIAA1217" "LRRC4B"  
## [25] "HAVCR2"   "MICAL1"   "ARHGAP26" "SNTG1"    "SLC43A1"  "TBX6"    
## [31] "FSIP1"    "CNKSR3"   "FBXO32"   "C2CD2"    "DHRSX"    "REPS2"   
## [37] "SYNM"     "ANKS1B"   "HAUS7"   
## [1] "found 39 genes."

## [1] 2
##  [1] "ANKRD24"        "SPATA6L"        "TFAP2E"         "DNAH12"        
##  [5] "HDHD5-AS1"      "MAMDC2-AS1"     "LEFTY1"         "RP11-1252I4.2" 
##  [9] "RP4-785G19.5"   "RP11-20I20.2"   "IDH2-DT"        "RP11-396B14.2" 
## [13] "SYNPO2L-AS1"    "RP5-965G21.3"   "P2RX7"          "CATSPERG"      
## [17] "AGFG2"          "NKD1"           "GAL3ST2"        "ADCY8"         
## [21] "CFAP251"        "ZNF653"         "DHRS3"          "C2"            
## [25] "TVP23A"         "NAV2"           "GNG4"           "C7orf61"       
## [29] "CCDC30"         "TRPV1"          "LINC00862"      "DISP3"         
## [33] "ODAD4"          "ARL17B"         "RP11-348F1.3"   "LINC00342"     
## [37] "LINC00884"      "LINC01137"      "EPCAM-DT"       "KCNK15-AS1"    
## [41] "RP11-60A24.3"   "CTD-2189E23.1"  "RP11-465L10.14" "RP11-125C10.1" 
## [1] "found 22 genes."

## [1] 3
##  [1] "NRXN3"         "RPH3A"         "PEX5L"         "UNC13A"       
##  [5] "CALY"          "NDST3"         "GRIK2"         "FSTL5"        
##  [9] "NRG4"          "MTSS1"         "GRIK1"         "NEGR1"        
## [13] "ERICH3"        "CCSER1"        "NAP1L3"        "CYP4X1"       
## [17] "PCLO"          "ERC2"          "GRM7"          "FBXO16"       
## [21] "RP11-170M17.1" "MSC-AS1"       "CXXC4-AS1"     "LINC02217"    
## [25] "RP4-809F18.1"  "RP11-413N10.3" "RP11-640F22.1" "RP11-320L2.1" 
## [29] "RP11-335E8.3"  "RIMS1"         "SEC14L5"       "PDE1A"        
## [33] "RIMS3"         "NLGN1"         "RIMS2"         "SYN3"         
## [37] "PTPRT"         "MMP17"         "CYP1B1-AS1"    "RP11-147G16.1"
## [41] "LINC01322"     "PCAT1"         "RP11-4D11.1"  
## [1] "found 29 genes."

## [1] 4
##  [1] "BID"      "FAR2"     "SRPX"     "CLIC5"    "CRISPLD1" "EEPD1"   
##  [7] "MASP1"    "FADS2"    "PTH1R"    "IGFBP7"   "HESX1"    "METTL2B" 
## [13] "TMEM130"  "GPC6"     "ARHGAP8"  "PTPRN"    "EBF4"     "DOK5"    
## [19] "RASL12"   "BNIP3L"   "KLHL29"   "NCAN"     "GFPT2"    "ARID5B"  
## [25] "KCNE4"    "MYO1E"    "SPTBN4"   "OXR1"     "ABCA3"    "KIF5C"   
## [31] "CLIC4"    "IFFO2"    "NPAS2"    "PFKFB3"   "FRMD5"    "RGMA"    
## [37] "DUSP8"    "ZBTB7C"   "TRDN"     "RASGEF1A" "RNF208"  
## [1] "found 41 genes."

## [1] 5
##  [1] "MAMLD1"        "HHAT"          "AHRR"          "MROH8"        
##  [5] "PEBP4"         "EFCAB11"       "GULP1"         "KIAA1328"     
##  [9] "ZBTB44-DT"     "CASC2"         "RFLNA"         "COL25A1"      
## [13] "RFX8"          "FIRRE"         "LIPE-AS1"      "LINC02649"    
## [17] "AC105760.2"    "TARID"         "AC008269.2"    "COX10-AS1"    
## [21] "RP11-550I24.2" "DRAIC"         "CTB-161M19.4"  "LINC02615"    
## [25] "RP11-266O8.1"  "SPESP1"        "RP11-111A21.1" "CRTC3-AS1"    
## [29] "GEMIN7-AS1"    "PLS3-AS1"      "RP11-96C13.1"  "RP4-681L3.3"  
## [33] "NIPAL3"        "DOCK10"        "NRG2"          "FAAH2"        
## [37] "TMEM229B"      "WARS2-AS1"     "LINC01135"     "DPH6-DT"      
## [41] "AC079610.1"    "RP11-379B18.8" "RP11-799O21.2"
## [1] "found 17 genes."

## [1] 6
##  [1] "SNCAIP"        "MAOB"          "SEMA3A"        "SYTL4"        
##  [5] "IQCH"          "DPYSL3"        "TACR1"         "LEPR"         
##  [9] "ACAT2"         "COL4A2"        "ABI3BP"        "PRTG"         
## [13] "VWA3B"         "HEG1"          "PROS1"         "F5"           
## [17] "LRRC24"        "RNF19A"        "SEMA3C"        "PIR"          
## [21] "SPAG1"         "FGL1"          "ST8SIA1"       "MAN1A1"       
## [25] "UST"           "SERPINI2"      "PRRX1"         "COL21A1"      
## [29] "PRR12"         "FCHO1"         "COL6A2"        "LMNTD1"       
## [33] "SEMA3D"        "DPYSL5"        "ELAPOR2"       "TMC1"         
## [37] "NPNT"          "ZFP36L1"       "CPEB1"         "RP11-190P13.2"
## [41] "CTD-2054N24.2"
## [1] "found 39 genes."

## [1] 7
##  [1] "CAP2"                  "TACC2"                 "FAXC"                 
##  [4] "LMOD1"                 "NXN"                   "SLC43A2"              
##  [7] "CCBE1"                 "C9orf153"              "TRMT9B"               
## [10] "MAP3K9"                "GTF2IRD1"              "HDAC9"                
## [13] "PDZD4"                 "MYO9B"                 "SYT17"                
## [16] "ARHGEF18"              "AEBP1"                 "WASF1"                
## [19] "PACRG"                 "IL1R1"                 "ZC4H2"                
## [22] "HIP1"                  "ZBTB46"                "IRAK2"                
## [25] "KIAA0513"              "CCDC40"                "MVB12A"               
## [28] "CLVS2"                 "RHPN1"                 "TMCO4"                
## [31] "PIK3CD"                "MOB3A"                 "HAP1"                 
## [34] "RILPL1"                "COL27A1"               "NHSL2"                
## [37] "MEF2B"                 "LYRM4"                 "RP11-513I15.6"        
## [40] "FBXO17"                "DGCR5_ENSG00000273032" "CASTOR2"              
## [1] "found 40 genes."

## [1] 8
##  [1] "ZFR2"           "ST6GALNAC5"     "CABLES1"        "ABHD3"         
##  [5] "ANKRD33B"       "ADRA1B"         "HOPX"           "TAFA1"         
##  [9] "SLIT1"          "SULT1A2"        "PPP1R26-AS1"    "RP11-390F4.6"  
## [13] "RP11-380P13.1"  "MTRNR2L8"       "AC005786.7"     "ADGRL1"        
## [17] "TRHDE"          "CACNA1I"        "XYLT1"          "PADI2"         
## [21] "TGIF2"          "TICAM1"         "RAP1GAP2"       "RHBDL3"        
## [25] "ADAMTS10"       "ST3GAL2"        "CSDC2"          "GNG7"          
## [29] "CTD-2527I21.15" "SPACA6"         "OSBP2"          "NOTUM"         
## [33] "AJAP1"          "NRSN2-AS1"      "HPN-AS1"        "AC004951.6"    
## [37] "HMGA1P4"        "RP5-827C21.2"   "RP11-346L1.2"   "LINC02356"     
## [41] "RP3-414A15.10"  "MAFG-DT"        "ATP6V0D1-DT"    "RP11-514P8.10" 
## [1] "found 28 genes."

## [1] 9
##  [1] "EPHA6"          "ENOX1"          "UNC79"          "TMEM132B"      
##  [5] "C4orf19"        "MN1"            "ANO5"           "MACROD2"       
##  [9] "LRRC3B"         "APTR"           "LCNL1"          "AP001628.6"    
## [13] "RP11-498J9.2"   "OBI1-AS1"       "RP11-410D17.2"  "CTC-329D1.2"   
## [17] "LINC01950"      "RP11-582J16.4"  "LINC00923"      "MGAM"          
## [21] "RP11-524F11.2"  "CTD-2349P21.11" "RP11-437L7.2"   "RP11-1289C17.1"
## [25] "RP11-215I16.3"  "ATP1A2"         "RNF24"          "TENM2"         
## [29] "ENOX2"          "ZMAT3"          "ARPP21"         "EFNA5"         
## [33] "PLK5"           "TPCN1"          "C3orf35"        "RP11-305L7.3"  
## [37] "KCNMB2-AS1"     "RP5-921G16.1"   "LINC01252"      "RP11-298I3.1"  
## [41] "AGBL1"          "RP11-711K1.8"  
## [1] "found 21 genes."

## [1] 10
##  [1] "TRPM3"    "GALNT16"  "EFEMP1"   "GTDC1"    "TMEM108"  "CXCL14"  
##  [7] "ACSL1"    "WIF1"     "VWCE"     "TMEM51"   "RNLS"     "KLHL32"  
## [13] "BRINP2"   "RARB"     "TGFB2"    "PALM"     "MYOM1"    "EEF2K"   
## [19] "KAT8"     "PPP1R13L" "ISYNA1"   "PPARGC1A" "TPD52L1"  "TFDP2"   
## [25] "B4GALT2"  "FOXO3"    "SLC39A11" "VAV3"     "CCNH"     "TIAM2"   
## [31] "FAM171A1" "ZEB1"     "CNNM2"    "FOXO1"    "FAM107A"  "ZNF608"  
## [37] "CRADD"    "TCAP"     "PARVA"    "ZNF358"   "EFCAB2"   "EML6"    
## [1] "found 42 genes."

## [1] 11
##  [1] "CD38"          "REEP1"         "SP140"         "ANKRD7"       
##  [5] "PLAGL1"        "H3-3B"         "BEND6"         "BTG2"         
##  [9] "VWA3A"         "PLD5"          "PRELID2"       "SLC4A5"       
## [13] "LGALSL-DT"     "LINC01630"     "RP11-106M7.1"  "LINC00407"    
## [17] "CDKN2B-AS1"    "BAALC-AS1"     "LINC02234"     "C5orf17"      
## [21] "OSMR-AS1"      "RP11-157I4.4"  "MPPED2-AS1"    "RP11-363J20.2"
## [25] "RP11-798K3.2"  "LINC00907"     "CTC-513N18.6"  "RP11-355F16.1"
## [29] "LINC01374"     "ARRDC3-AS1"    "BCL6-AS1"      "CTD-2313D3.2" 
## [33] "RP11-125D12.3" "RP11-592G13.2" "RP11-341N18.1" "TLE2"         
## [37] "USP9Y"         "PDPN"          "NLGN4Y"        "TTTY14"       
## [41] "UTY"           "TTTY10"        "RP5-1198O20.4" "LINC00278"    
## [1] "found 17 genes."

## [1] 12
##  [1] "KIRREL3"       "GALNTL6"       "LINC00326"     "KIF5C-AS1"    
##  [5] "CTD-2126E3.6"  "SYT7"          "KLHL4"         "ATRNL1"       
##  [9] "SCN2A"         "UNC13C"        "AK7"           "CBLN2"        
## [13] "SLC4A10"       "CDH18"         "CNTN5"         "ZNF385D"      
## [17] "SLC24A2"       "CFAP161"       "SHROOM4"       "LRRC2"        
## [21] "HTR1E"         "SLC38A11"      "SEMA3E"        "SLC8A1"       
## [25] "KCNH7"         "RTN4RL1"       "PDE2A"         "CACNA1E"      
## [29] "TNFRSF25"      "AC023469.1"    "RP11-191L9.4"  "RP1-30E17.2"  
## [33] "RP11-563D10.1" "KRTAP5-AS1"    "AC067956.1"    "SHISA9"       
## [37] "AC002066.1"    "CTC-340A15.2"  "LINC02223"     "RP11-79E3.2"  
## [41] "RP11-624C23.1" "RP11-958J22.1" "RP11-596C23.6" "IQCJ-SCHIP1"  
## [1] "found 28 genes."

## [1] 13
##  [1] "ATP11A"       "MAP2K6"       "MGAT3"        "PRR5L"        "FAM117B"     
##  [6] "SLC44A3"      "C4orf45"      "PBX3"         "LRRN2"        "CTA-292E10.6"
## [11] "HGF"          "SAMD4A"       "APBA2"        "CDON"         "PDK3"        
## [16] "TMEM38A"      "ITPKC"        "RELB"         "OLFM2"        "PLIN3"       
## [21] "RFTN1"        "ZSWIM4"       "NFIC"         "ENSA"         "BOC"         
## [26] "ZNF208"       "FBXO27"       "SHISA5"       "PKNOX2"       "FRMD3"       
## [31] "SYT12"        "PACS1"        "CMTM4"        "DMWD"         "TCEA3"       
## [36] "LINC00685"    "RP5-864K19.4" "L3MBTL2-AS1"  "OLMALINC"     "RP1-158P9.2" 
## [41] "MIR23AHG"     "RP11-404C6.6"
## [1] "found 34 genes."

## [1] 14
##  [1] "UPP2"          "MOGAT1"        "DPH6"          "CD72"         
##  [5] "MAP3K7CL"      "RHCE"          "CRPPA"         "POT1-AS1"     
##  [9] "LNC-LBCS"      "LINC01185"     "MIR181A1HG"    "MMADHC-DT"    
## [13] "RP11-120D5.1"  "RPL34-DT"      "NPIPB2"        "SUCLG2-AS1"   
## [17] "RP11-11N9.4"   "RP11-130F10.1" "RP11-268P4.5"  "RP11-284M14.1"
## [21] "LINC01182"     "MAILR"         "RP11-156K13.1" "RP11-20E24.1" 
## [25] "RP11-397A16.1" "RP11-436D23.1" "RP11-281A20.2" "RP11-382N13.7"
## [29] "RP11-692P14.1" "RP11-444C24.1" "RP11-563M4.2"  "CTD-2297M2.1" 
## [33] "STAG1"         "PDE3A"         "LSMEM2"        "AP000318.2"   
## [37] "LINC00598"     "AC104088.1"    "ARHGEF26-AS1"  "STX18-AS1"    
## [41] "CASC17"        "TAPT1-AS1"     "RP11-26L21.1"  "RP11-166M16.1"
## [1] "found 11 genes."

## [1] 15
##  [1] "PRKAR2B"  "ARHGAP44" "TENM1"    "ELAVL2"   "MLIP"     "SETBP1"  
##  [7] "SHANK2"   "RGS7"     "KCTD16"   "SMYD3"    "DLGAP2"   "SYT1"    
## [13] "RBFOX1"   "UBE2R2"   "ZMIZ1"    "CPE"      "HIVEP3"   "QRICH2"  
## [19] "DPP6"     "SOX5"     "TTLL7"    "ZNF385B"  "DIAPH2"   "CACNA1B" 
## [25] "SHANK1"   "ABLIM2"   "RBFOX3"   "FRMPD4"   "DLGAP1"   "CNTNAP2" 
## [31] "SAMD12"   "RGS6"     "CSMD1"    "OPCML"    "RALYL"    "KCNQ5"   
## [37] "KCNIP4"   "ELAVL3"   "ARID5A"   "RYR2"     "MEG3"    
## [1] "found 40 genes."

## [1] 16
##  [1] "XK"            "MAEL"          "PAH"           "GPR39"        
##  [5] "CC2D2B"        "DCHS2"         "DIO2"          "RP11-306O13.1"
##  [9] "AP000233.4"    "LINC01117"     "PLCG1-AS1"     "AC012593.1"   
## [13] "SOX21-AS1"     "LINC01344"     "AC007682.1"    "LINC01937"    
## [17] "AC009264.1"    "RP11-142A5.1"  "AC079305.11"   "RP11-154H17.1"
## [21] "RP11-373N22.3" "LINC02144"     "RP11-669M16.1" "RP11-679C8.2" 
## [25] "RP11-404I7.2"  "RP1-84O15.2"   "LINC00534"     "ZFHX4-AS1"    
## [29] "RP11-804N13.1" "RP11-541P9.3"  "RP11-431M3.1"  "LINC02763"    
## [33] "RMST"          "RP11-260G13.1" "RP11-526N18.1" "RP11-242P2.1" 
## [37] "CTC-498M16.4"  "RP11-561I11.4" "LINC01727"     "CH17-174L20.1"
## [41] "RP11-313M3.2"  "RP3-383B8.1"   "RP11-346I3.7"  "AC006296.4"   
## [45] "RP11-399K19.1"
## [1] "found 7 genes."

## [1] 17
##  [1] "MBNL3"     "GABRA4"    "HSD11B1"   "HS3ST3B1"  "GPNMB"     "ABCA12"   
##  [7] "ARHGAP27"  "AXDND1"    "AGBL2"     "ZCCHC18"   "EPHX4"     "C1QTNF4"  
## [13] "SP140L"    "WNT7B"     "HES5"      "L3MBTL3"   "SAMD13"    "BAALC-AS2"
## [19] "PDXP"      "DCN"       "ABCA7"     "ZFY"       "ANGPT2"    "PCDH11Y"  
## [25] "TNNT2"     "TBX2"      "AIF1L"     "EDA2R"     "C1QL1"     "SLC6A6"   
## [31] "FREM2"     "KCNJ16"    "CATIP"     "SPATA2L"   "ZER1"      "LRRC8C"   
## [37] "NXNL1"     "MB21D2"    "PCP4"      "ETV5"     
## [1] "found 39 genes."

## [1] 18
##  [1] "PNPLA3"   "LYPD6B"   "DPP10"    "CNTN1"    "RIMBP2"   "CTNNA2"  
##  [7] "CAB39L"   "TUSC3"    "GLIS3"    "CHRNE"    "CLNK"     "SGK1"    
## [13] "PLXDC2"   "HIF3A"    "AHNAK"    "GALNT8"   "RIN2"     "ARHGEF4" 
## [19] "PLCE1"    "SSH2"     "BCAS3"    "GABPB2"   "KCNN3"    "DOCK11"  
## [25] "ITPRIP"   "GRIK4"    "RASSF3"   "NCAM2"    "ABR"      "ZNF704"  
## [31] "ABCA1"    "WNK2"     "SLC20A2"  "FAM222B"  "SH3PXD2B" "PPM1E"   
## [37] "PHYHD1"   "SWI5"     "TSHZ2"    "NHS"      "SRGAP1"   "S100A10" 
## [43] "NEAT1"   
## [1] "found 42 genes."

## [1] 19
##  [1] "WDR64"         "GLIPR1L1"      "FSIP2"         "ANKUB1"       
##  [5] "RNF212B"       "AC002463.3"    "RP11-131L23.1" "RP4-660H19.1" 
##  [9] "RP11-547I7.1"  "ST7-AS2"       "ASTN2-AS1"     "RP11-141A19.1"
## [13] "CCDC192"       "GPC5-AS2"      "PCDH9-AS4"     "RP11-666F17.1"
## [17] "LINC02250"     "AC008067.2"    "RP11-475C16.2" "RP13-143G15.4"
## [21] "LINC02877"     "LINC00960"     "RP11-768G7.3"  "RP11-115N4.1" 
## [25] "LRP4-AS1"      "ANK2-AS1"      "RP11-223C24.1" "MAPK10-AS1"   
## [29] "RP11-120A1.1"  "RP11-116O11.1" "RP11-351A11.1" "RP11-463D19.1"
## [33] "RP11-513G19.1" "A2ML1-AS1"     "RP11-370I10.2" "RP11-887P2.5" 
## [37] "DIO2-AS1"      "RP11-58G13.1"  "RP11-138H11.1" "CTD-2282P23.2"
## [41] "CH17-140K24.2" "RP11-576O3.1"  "RP11-394G3.3"  "RP11-66G15.1" 
## [1] "found 6 genes."

## [1] 20
##  [1] "PAPPA2"        "MTERF1"        "PKIB"          "SAXO1"        
##  [5] "PKD1L1"        "FREM1"         "SCN11A"        "RNF212"       
##  [9] "CLDN4"         "SCOC-AS1"      "LEKR1"         "RP11-344B5.2" 
## [13] "AC072062.3"    "LINC00271"     "RFX3-AS1"      "AF131217.1"   
## [17] "LINC01239"     "LINC01524"     "RP11-195C7.1"  "LINC01376"    
## [21] "LINC01695"     "LINC02652"     "RP11-132E11.2" "LINC01358"    
## [25] "RP11-624M8.1"  "H2AZ1-DT"      "LINC02355"     "LINC01340"    
## [29] "LIX1-AS1"      "C8orf37-AS1"   "RP11-708B6.2"  "RP11-511B23.2"
## [33] "RP11-352M15.1" "LINC02320"     "RP11-16B13.1"  "RP11-739G5.1" 
## [37] "PSMD7-DT"      "RP11-571L19.7" "RP11-157E16.1" "CTC-490G23.6" 
## [41] "RP11-964E11.3" "RP11-274G22.1" "RP11-221G19.1" "RP5-892C22.1" 
## [45] "RP11-446J8.1" 
## [1] "found 10 genes."

## [1] 21
##  [1] "CALCRL"        "CCDC80"        "PLCB4"         "SLC16A6"      
##  [5] "IFI44L"        "SLC24A4"       "ADAMTS9"       "GUCY1A1"      
##  [9] "DELEC1"        "CYP4F12"       "CYP4F3"        "STUM"         
## [13] "INSYN2B"       "RP11-735G4.1"  "LINC01515"     "LINC01768"    
## [17] "DIRC3-AS1"     "AC007563.5"    "AC092684.1"    "SOCS2-AS1"    
## [21] "NEUROG2-AS1"   "VCAN-AS1"      "LINC02715"     "MAP1LC3B2"    
## [25] "RP11-116N8.1"  "FRMD6-AS2"     "PTCSC3"        "DISC1FP1"     
## [29] "RP11-793A3.2"  "RP11-354K4.2"  "RP11-323P17.2" "RP11-290O12.2"
## [33] "LINC00836"     "LINC00842"     "RP11-364P22.4" "RP11-373E16.6"
## [37] "RP11-259G3.1"  "RP11-154D6.3"  "RP11-609L3.3"  "RP1-20N4.2"   
## [41] "RP11-423B13.1" "RP11-469A15.2" "RP11-114N1.1" 
## [1] "found 13 genes."

## [1] 22
##  [1] "PRKCQ"        "SDK2"         "CEMIP"        "GBE1"         "AKAP12"      
##  [6] "EPSTI1"       "GALNT10"      "STOX2"        "CA8"          "EXT1"        
## [11] "CMSS1"        "GCNT1"        "TENM3"        "MALAT1"       "MCF2L2"      
## [16] "PLXNA2"       "KIF3C"        "HSD17B14"     "PCSK5"        "NAMPT"       
## [21] "LIN7A"        "ZSWIM6"       "ADGRB3"       "ARHGAP29"     "SLC44A5"     
## [26] "PCSK6"        "PTPRJ"        "ABCB9"        "THRB"         "JAZF1"       
## [31] "ADORA1"       "PCDH7"        "ALK"          "CADM2"        "NCKAP5"      
## [36] "SLC25A20"     "CADM1"        "ABAT"         "ARL15"        "DNM3"        
## [41] "TMEM161B-AS1"
## [1] "found 39 genes."

## [1] 23
##  [1] "CPED1"                 "BICC1"                 "SLC14A1"              
##  [4] "UNC5D"                 "LRRIQ3"                "LINC01266"            
##  [7] "LMCD1-AS1"             "AC097721.2"            "LINC00877"            
## [10] "RFX2"                  "SLC26A3"               "DAAM1"                
## [13] "CDH20"                 "STEAP1B"               "LGI1"                 
## [16] "RFX4"                  "LRMDA"                 "PLCL2"                
## [19] "GPR176"                "GSG1L"                 "IQCK"                 
## [22] "PPP1R42"               "APOLD1"                "FIGN"                 
## [25] "LHFPL6"                "MAML2"                 "FLRT2"                
## [28] "FAM174B"               "NKAIN2"                "KIF9-AS1"             
## [31] "LINC01320"             "RP11-154D17.1"         "RP11-17A1.3"          
## [34] "LINC02742"             "LINC01609"             "RP11-20D14.3"         
## [37] "RPPH1_ENSG00000259001" "LINC00558"             "RP11-838N2.5"         
## [40] "RMRP_ENSG00000269900"  "CH507-528H12.1"        "RP4-799O8.1"          
## [43] "AC003099.2"            "RP11-398J12.1"        
## [1] "found 25 genes."

## [1] 24
##  [1] "CDH10"         "EPB41L4B"      "SCG3"          "DHRS7B"       
##  [5] "SLC1A2"        "DNAH7"         "C10orf90"      "MTCL1"        
##  [9] "SNTB1"         "TMEM132C"      "ROR1"          "SHISA6"       
## [13] "RP11-496B10.6" "ARHGAP31"      "COL23A1"       "RRP12"        
## [17] "SYNE2"         "DGKG"          "SESN1"         "PHACTR3"      
## [21] "COBL"          "CPEB3"         "C1orf21"       "WLS"          
## [25] "PDZRN3"        "TOX2"          "TNS3"          "SLC22A23"     
## [29] "SHROOM3"       "GLTP"          "MAPK4"         "SDK1"         
## [33] "FAM13C"        "ADAM33"        "DOC2A"         "PID1"         
## [37] "GNA14"         "AHCYL2"        "CACNB2"        "ZFPM2"        
## [41] "ZNF785"        "TOX"          
## [1] "found 41 genes."

## [1] 25
##  [1] "PUDP"          "RERG"          "OTOGL"         "SGCD"         
##  [5] "SLC24A3"       "GRM3"          "AC074391.1"    "SOX1-OT"      
##  [9] "EPS15-AS1"     "AP000282.2"    "LINC01934"     "LINC00886"    
## [13] "HS3ST5"        "LINC02196"     "F11-AS1"       "LINC00499"    
## [17] "LINC01301"     "RP11-317N12.1" "GS1-57L11.1"   "RP11-134O21.1"
## [21] "LINC00540"     "RP11-378A12.1" "RP11-624A4.2"  "COL5A3"       
## [25] "GRK3"          "HPSE2"         "CALCB"         "FZD8"         
## [29] "NME9"          "ZNF98"         "AC064875.2"    "AC003991.3"   
## [33] "SPRY4-AS1"     "AC002127.4"    "PDYN-AS1"      "MEIKIN"       
## [37] "RTL9"          "ALDH1L1-AS2"   "LINC02208"     "LINC01414"    
## [41] "RP11-328J6.1"  "RP11-237N2.1"  "RP11-421A16.1" "RP11-183J19.1"
## [1] "found 16 genes."

## [1] 26
##  [1] "IL7"           "CA1"           "LINC01931"     "SHOC1"        
##  [5] "FILIP1L"       "P2RY14"        "HEPN1"         "TMLHE-AS1"    
##  [9] "AC105461.1"    "AC017101.10"   "RP11-417B4.2"  "GNA14-AS1"    
## [13] "RP11-46O21.2"  "GRM3-AS1"      "LINC00513"     "AC037445.1"   
## [17] "RP11-109I13.2" "RBMS3-AS3"     "STARD13-AS"    "GS1-433O24.1" 
## [21] "LINC01877"     "RP11-657O9.1"  "ZBTB20-AS5"    "GK-AS1"       
## [25] "RP11-274H2.2"  "RORA-AS1"      "LUCAT1"        "RP11-39E3.3"  
## [29] "ZFPM2-AS1"     "STPG2-AS1"     "CTD-3239E11.2" "BBOX1-AS1"    
## [33] "CTD-2537O9.1"  "RP11-1H15.2"   "AP000462.2"    "RP11-315E17.1"
## [37] "RP11-39M21.1"  "CRIM1-DT"      "PRKCA-AS1"     "RP11-555K12.4"
## [41] "SLC5A11"       "LINGO1"        "LINC01208"     "AC013463.2"   
## [1] "found 8 genes."

## [1] 27
##  [1] "FAM107B"       "SLC22A3"       "RNF150"        "LINC01876"    
##  [5] "XIST"          "LINC02884"     "CTXND1"        "RP11-175O15.1"
##  [9] "RASGRP2"       "ARHGAP15"      "RIPOR2"        "TFCP2L1"      
## [13] "ACVR1C"        "SEM1"          "IQCA1"         "DMGDH"        
## [17] "LGR6"          "MRAS"          "ESYT3"         "VWA5B1"       
## [21] "RFTN2"         "RANBP3L"       "PTCHD1"        "FAXDC2"       
## [25] "CHST11"        "LDLRAD3"       "SLC25A18"      "POTEG"        
## [29] "NWD1"          "OSTN"          "TMEM184B"      "PLIN5"        
## [33] "STARD10"       "LINC00511"     "DLEU2"         "PTCHD1-AS"    
## [37] "AC016745.3"    "RP11-507B12.2" "RP11-507B12.1" "MTRNR2L12"    
## [41] "CH507-513H4.1" "LINC02246"     "RP11-358F13.1" "RP1-166D18.1" 
## [1] "found 30 genes."

## [1] 28
##  [1] "WNT5B"         "PDE10A"        "F3"            "GDAP1L1"      
##  [5] "TMEM241"       "PDE5A"         "MEGF11"        "HHIP"         
##  [9] "SEPTIN1"       "PNMA3"         "SGCZ"          "EYS"          
## [13] "HES4"          "NPSR1-AS1"     "KCNMB2"        "RP1-292B18.4" 
## [17] "SNAP25-AS1"    "RP1-45C12.1"   "LINC01829"     "LINC01618"    
## [21] "RP11-673E1.1"  "RP11-586K2.1"  "AB015752.3"    "LINC02389"    
## [25] "LINC02254"     "RP11-103J8.1"  "RP11-314E10.1" "USH2A"        
## [29] "RHOBTB1"       "LAMB4"         "WFDC1"         "PXDNL"        
## [33] "GREM1"         "MRGPRF"        "ZNF804B"       "FZD9"         
## [37] "HRAT92"        "LINC02869"     "RP11-384F7.1"  "LINC01619"    
## [41] "CEACAM16-AS1"  "PKD1L3"        "RP11-93B21.2" 
## [1] "found 24 genes."

## [1] 29
##  [1] "PON3"          "TENT5A"        "AGBL3"         "SLC9B1"       
##  [5] "C12orf42"      "CATSPERE"      "LINC01006"     "RANBP17"      
##  [9] "COL28A1"       "AC026188.1"    "RP1-15D23.2"   "HDAC2-AS2"    
## [13] "PCDH9-AS2"     "LINC01277"     "CCDC26"        "UFL1-AS1"     
## [17] "PPP1R9A-AS1"   "RNF217-AS1"    "PKN2-AS1"      "RP11-4B14.3"  
## [21] "RP5-1101C3.1"  "PTPRG-AS1"     "NECTIN3-AS1"   "RP11-167H9.4" 
## [25] "MEF2C-AS2"     "LINC00504"     "RP11-436F23.1" "RP11-649G15.2"
## [29] "RP11-624D11.2" "CENATAC-DT"    "PRANCR"        "RP11-72M17.1" 
## [33] "LINC01579"     "RP11-525K10.3" "LINC01572"     "TSIX"         
## [37] "LINC02664"     "RP11-470M1.2"  "RP11-57G22.3"  "RP11-69G16.2" 
## [41] "RP4-660H19.2"  "RP1-84D21.2"   "RP11-120J1.2"  "RP11-168F16.1"
## [1] "found 8 genes."

## [1] 30
##  [1] "PHACTR2"                 "FHAD1"                  
##  [3] "HS3ST3A1"                "PCED1B"                 
##  [5] "RP1-167A14.2"            "APP-DT"                 
##  [7] "SLCO1A2"                 "CLIP2"                  
##  [9] "JHY"                     "BEST3"                  
## [11] "PATJ"                    "TMTC1"                  
## [13] "TTC9"                    "DGKB"                   
## [15] "GMPR"                    "DENND2A"                
## [17] "CCDC3"                   "LRGUK"                  
## [19] "DRC1"                    "ORAI2"                  
## [21] "SYTL3"                   "ADCY1"                  
## [23] "ARMC3"                   "DEPP1"                  
## [25] "PDZRN4"                  "TEKT1"                  
## [27] "ATOH8"                   "COL24A1"                
## [29] "RCAN2"                   "PRIMA1"                 
## [31] "SPATA13_ENSG00000182957" "SHTN1"                  
## [33] "CFAP54"                  "LINC00632"              
## [35] "S1PR3"                   "AC003090.1"             
## [37] "AP001347.6"              "AL163953.3"             
## [39] "LINC02315"               "LINC01094"              
## [41] "ZNF594-DT"               "KLF2-DT"                
## [43] "RP11-35G9.5"             "SCARNA2_ENSG00000270066"
## [45] "RP11-154H23.4"          
## [1] "found 31 genes."

## [1] 31
##  [1] "NTN1"       "SEZ6L"      "SLC39A14"   "RGS4"       "TRIM5"     
##  [6] "TESPA1"     "RNF165"     "PLK2"       "ARHGAP18"   "PLEKHG4B"  
## [11] "MMP16"      "SYNPR"      "FABP5"      "KCNB2"      "STAC3"     
## [16] "PIWIL2"     "AC011288.2" "KCNG1"      "CDH3"       "CELF4"     
## [21] "SLC7A5"     "MPP6"       "TSPAN11"    "NRP2"       "SPP1"      
## [26] "HS3ST2"     "PMEPA1"     "LOXL1"      "SRRM4"      "KCNH5"     
## [31] "ITPR1"      "RIT2"       "FGF17"      "PTMS"       "ZMAT4"     
## [36] "MAP1A"      "VAT1L"      "NABP1"      "ST8SIA3"    "VSTM2B"    
## [41] "MTRNR2L1"  
## [1] "found 40 genes."

## [1] 32
##  [1] "USH1C"    "DNAH9"    "GAB2"     "SH3D19"   "PPM1H"    "UBE3D"   
##  [7] "BEX2"     "BTBD11"   "MIPOL1"   "NDUFAF2"  "ABTB2"    "TSPAN5"  
## [13] "ALCAM"    "GPR156"   "ADAP2"    "AQP1"     "SLC7A2"   "PDE4A"   
## [19] "ATP2B3"   "RASAL2"   "MAST3"    "CDKL1"    "COTL1"    "SH3PXD2A"
## [25] "ARSB"     "TMCC2"    "NAV1"     "CCDC146"  "CDR2"     "ITPKB"   
## [31] "PAM"      "MAGI1"    "AKAP6"    "ART3"     "TIAM1"    "GDPD5"   
## [37] "ITGA2"    "EDIL3"    "PLEKHA7"  "STX8"     "SLC35E3"  "ANO6"    
## [43] "C19orf38"
## [1] "found 42 genes."

## [1] 33
##  [1] "CHODL"         "STK32A"        "BNC2"          "LINC02814"    
##  [5] "RP11-364L4.3"  "RP11-492O8.3"  "ARHGAP6"       "ST6GALNAC2"   
##  [9] "ST6GAL1"       "FAP"           "SOHLH2"        "LRAT"         
## [13] "KLF2"          "CCDC175"       "ANGPT1"        "SAMD3"        
## [17] "CFAP47"        "PPP1R36"       "METTL7B"       "CAVIN1"       
## [21] "PLCXD3"        "SAMD11"        "LAMA2"         "PLPP4"        
## [25] "CFI"           "RP11-174G6.1"  "RP1-111D6.3"   "RP11-146I2.1" 
## [29] "RP11-90C4.1"   "IQCM"          "LINC01411"     "LINC01088"    
## [33] "RP11-279O9.4"  "LINC00609"     "LINC02251"     "RP11-259K15.2"
## [37] "RP11-627D16.1" "RP11-876N24.2" "RP1-79C4.4"    "RP11-403A3.3" 
## [41] "RP11-403A3.2"  "RP11-542F9.2"  "RP11-301F14.1" "RP11-6L16.1"  
## [1] "found 23 genes."

## [1] 34
##  [1] "ASB4"     "MSMO1"    "CCDC85A"  "IDI1"     "SRBD1"    "BLVRB"   
##  [7] "PLS3"     "RPL18A"   "EPM2A"    "GMDS"     "LAMA4"    "ID2"     
## [13] "NID1"     "PPP1R3C"  "MT2A"     "ID1"      "IFI6"     "APOE"    
## [19] "RPL36"    "CCDC59"   "RPLP1"    "FAU"      "TEX9"     "GFRA1"   
## [25] "SYCP2L"   "HNF4G"    "ALDH1A1"  "RPS27"    "ZNF48"    "GINS3"   
## [31] "KIAA0825" "MT1X"     "PTMA"     "SNHG31"   "RPS18"    "MRPL33"  
## [37] "KNOP1"    "ARID3A"   "CKB"      "MITF"     "NOL4L"   
## [1] "found 40 genes."

## [1] 35
##  [1] "MRC2"     "RIPK2"    "NT5DC3"   "B3GAT2"   "ADCY7"    "EPHB2"   
##  [7] "AVIL"     "LPAR4"    "CCDC141"  "CA3"      "SVEP1"    "SCG5"    
## [13] "PAPPA"    "CP"       "ATP9A"    "FOSL2"    "GADD45B"  "NFATC2"  
## [19] "ABCC3"    "IGSF21"   "ID3"      "ITIH5"    "JUND"     "EGF"     
## [25] "CLSTN3"   "DEPTOR"   "ARHGAP35" "C1orf87"  "ATF3"     "TMEM200A"
## [31] "NFIL3"    "NT5DC2"   "JUNB"     "SPSB1"    "PLEKHG5"  "RND1"    
## [37] "PAWR"     "YOD1"     "FAM110C"  "MAFF"     "CRYBB2"  
## [1] "found 41 genes."

## [1] 36
##  [1] "BCAS1"          "SRPX2"          "LRRC9"          "LRTM1"         
##  [5] "CHST9"          "CLMP"           "MFSD4B"         "DLEU1"         
##  [9] "COL5A2"         "TSBP1"          "Z83001.1"       "RP4-613B23.1"  
## [13] "DPP10-AS3"      "AC009501.4"     "IPO9-AS1"       "GNG12-AS1"     
## [17] "DPP10-AS1"      "RP11-446H18.5"  "SEMA6A-AS1"     "RP11-114J13.1" 
## [21] "CTD-2015H6.3"   "RP11-348J24.1"  "RP11-517I3.1"   "RP11-711G10.1" 
## [25] "RP11-452H21.1"  "AP000487.6"     "RP11-867G2.8"   "RP11-144F15.1" 
## [29] "RP11-104E19.1"  "HIF1A-AS3"      "RP11-184D12.1"  "AC004158.3"    
## [33] "RP11-80I3.1"    "SLC7A14-AS1"    "CTC-428H11.2"   "RP11-589M4.5"  
## [37] "RP11-793H13.14" "RP5-847G17.1"   "CTD-2172F7.1"   "RP11-725F23.1" 
## [41] "RP11-255O19.2"  "RP11-875G18.1"  "NUP210L"        "OVCH1"         
## [45] "RP11-103P4.1"  
## [1] "found 11 genes."

## [1] 37
##  [1] "ANOS1"         "LRRC7"         "KCNN2"         "DNAH6"        
##  [5] "RGS22"         "KCTD1"         "LIX1"          "SPATA17"      
##  [9] "KIF6"          "JAM3"          "ODAD2"         "ENO4"         
## [13] "MAML3"         "MALRD1"        "CHL1-AS2"      "PATL2"        
## [17] "RP1-232L24.3"  "RP1-230L10.1"  "CTC-347C20.1"  "CTB-178M22.2" 
## [21] "ADGRL1-AS1"    "LINC00506"     "RP11-574F11.4" "RP11-788A4.3" 
## [25] "DNAH5"         "MOB3B"         "CNKSR2"        "HNMT"         
## [29] "FAM151B"       "TDRD9"         "FAT3"          "SLC26A5"      
## [33] "GPR137C"       "PAX8-AS1"      "TOGARAM2"      "TSBP1-AS1"    
## [37] "AC092155.4"    "RP11-69I8.3"   "RP1-35C21.2"   "MIR4300HG"    
## [41] "RP11-148E17.1" "RP11-210M15.2" "SPANXA2-OT1"   "RP11-114N19.3"
## [1] "found 24 genes."

## [1] 38
##  [1] "MT3"            "STS"            "MT1G"           "SUMF1"         
##  [5] "C2CD6"          "STPG2"          "CD200R1"        "C11orf65"      
##  [9] "MT1E"           "CYP7B1"         "SUGCT"          "HMGN5"         
## [13] "ADD3-AS1"       "MT1H"           "AC007277.3"     "AC004540.5"    
## [17] "LINC00571"      "MRPS9-AS2"      "RP11-162D16.2"  "LYPLAL1-DT"    
## [21] "ZRANB2-AS2"     "LINC01036"      "AC079807.4"     "RAP2C-AS1"     
## [25] "RP11-154D6.1"   "SOX2-OT"        "RP11-461O7.1"   "C1QTNF7-AS1"   
## [29] "RP11-124B13.1"  "LINC02740"      "RP11-727A23.10" "LINC02745"     
## [33] "LINC02326"      "LINC02327"      "LINC02328"      "LINC00637"     
## [37] "AC007193.6"     "RP11-520F22.1"  "KBTBD12"        "RP11-26J3.1"   
## [41] "RP11-150C16.1"  "CTD-2201E18.6"  "RP3-466I7.2"   
## [1] "found 14 genes."

## [1] 39
##  [1] "SIDT1"            "WSCD2"            "ARHGAP28"         "SLC8A3"          
##  [5] "KIAA1549L"        "ELL2"             "PLXNC1"           "RNF175"          
##  [9] "DUSP15"           "DNAAF1"           "RETREG1"          "GFRA2"           
## [13] "SNX31"            "DIRC3"            "LINC01725"        "LINC00958"       
## [17] "MAPT-AS1"         "MCUB"             "BAIAP3"           "VCAN"            
## [21] "KITLG"            "P3H2"             "CCL2"             "MAN1C1"          
## [25] "SCN1A"            "ST18"             "PARP8"            "NFASC"           
## [29] "ARHGEF3"          "SLITRK5"          "FBN1"             "TPST1"           
## [33] "SLCO3A1"          "CHST6"            "XXbac-BPG55C20.7" "SATB1-AS1"       
## [37] "CTD-2643I7.5"     "PTCHD4"           "CTB-35F21.1"      "LINC02506"       
## [41] "RP11-499F3.2"     "AF038458.3"       "RP5-1015P16.1"   
## [1] "found 31 genes."

## [1] 40
##  [1] "RRAGD"         "PSD"           "PCSK1N"        "POLR2I"       
##  [5] "RASD1"         "PDE8B"         "TRIM22"        "CHI3L1"       
##  [9] "FHDC1"         "WARS1"         "ITGA9"         "PRSS23"       
## [13] "SPOCK1"        "CIITA"         "WDR97"         "IER5L"        
## [17] "CARNMT1-AS1"   "RP1-223B1.1"   "LINC01503"     "PRKAR2B-AS1"  
## [21] "RP11-745L13.2" "RP1-41C23.1"   "PRAG1"         "RP11-239A17.1"
## [25] "CTD-2040G12.2" "GAS7"          "KLF6"          "FRY"          
## [29] "TESC"          "DNAH11"        "TSHZ3"         "HELB"         
## [33] "COL5A1"        "ADAM12"        "SEC24D"        "COX7A1"       
## [37] "PGM2L1"        "CCK"           "DPYD"          "SLC6A9"       
## [41] "SMOC1"         "MIR34AHG"      "RP1-187B23.1"  "RP3-365E2.1"  
## [1] "found 33 genes."

Session information

gc()

##           used  (Mb) gc trigger  (Mb) limit (Mb) max used  (Mb)
## Ncells 4161895 222.3    7959177 425.1         NA  7959177 425.1
## Vcells 8942726  68.3   29538339 225.4      65536 29518146 225.3

sessionInfo()

## R version 4.2.3 (2023-03-15)
## Platform: aarch64-apple-darwin20 (64-bit)
## Running under: macOS Ventura 13.4.1
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] stringr_1.5.0     limma_3.54.2      tidyr_1.3.0       ggpubr_0.6.0     
## [5] ggplot2_3.4.2     data.table_1.14.8
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_1.0.10            png_0.1-8              Biostrings_2.66.0     
##  [4] digest_0.6.31          utf8_1.2.3             R6_2.5.1              
##  [7] GenomeInfoDb_1.34.9    backports_1.4.1        stats4_4.2.3          
## [10] RSQLite_2.3.1          evaluate_0.20          httr_1.4.6            
## [13] pillar_1.9.0           zlibbioc_1.44.0        rlang_1.1.0           
## [16] rstudioapi_0.14        car_3.1-2              jquerylib_0.1.4       
## [19] blob_1.2.4             R.oo_1.25.0            R.utils_2.12.2        
## [22] S4Vectors_0.36.2       rmarkdown_2.21         labeling_0.4.2        
## [25] RCurl_1.98-1.12        bit_4.0.5              munsell_0.5.0         
## [28] broom_1.0.4            compiler_4.2.3         xfun_0.39             
## [31] pkgconfig_2.0.3        BiocGenerics_0.44.0    htmltools_0.5.5       
## [34] tidyselect_1.2.0       KEGGREST_1.38.0        GenomeInfoDbData_1.2.9
## [37] tibble_3.2.1           IRanges_2.32.0         fansi_1.0.4           
## [40] crayon_1.5.2           dplyr_1.1.2            withr_2.5.0           
## [43] R.methodsS3_1.8.2      bitops_1.0-7           grid_4.2.3            
## [46] jsonlite_1.8.4         gtable_0.3.3           lifecycle_1.0.3       
## [49] DBI_1.1.3              magrittr_2.0.3         scales_1.2.1          
## [52] cli_3.6.1              stringi_1.7.12         cachem_1.0.7          
## [55] carData_3.0-5          farver_2.1.1           XVector_0.38.0        
## [58] ggsignif_0.6.4         bslib_0.4.2            generics_0.1.3        
## [61] vctrs_0.6.2            RColorBrewer_1.1-3     org.Hs.eg.db_3.16.0   
## [64] tools_4.2.3            bit64_4.0.5            Biobase_2.58.0        
## [67] glue_1.6.2             purrr_1.0.1            abind_1.4-5           
## [70] fastmap_1.1.1          yaml_2.3.7             AnnotationDbi_1.60.2  
## [73] colorspace_2.1-0       rstatix_0.7.2          memoise_2.0.1         
## [76] knitr_1.44             sass_0.4.5